From d520195552bb8861ff3c5e6bf835e6b5db829e76 Mon Sep 17 00:00:00 2001
From: gnefedev <georgynefedev@gmail.com>
Date: Wed, 5 Apr 2023 08:40:50 +0200
Subject: [PATCH 1/3] don't cut features on export library

---
 .../mixcr/cli/CommandFindAlleles.kt           | 28 ++++---------------
 1 file changed, 6 insertions(+), 22 deletions(-)

diff --git a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt
index 8ecea8f3b..1edc1094f 100644
--- a/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt
+++ b/src/main/kotlin/com/milaboratory/mixcr/cli/CommandFindAlleles.kt
@@ -445,28 +445,12 @@ class CommandFindAlleles : MiXCRCommandWithOutputs() {
             primaryGenes
                 .sortedBy { it.name }
                 .forEach { gene ->
-                    val geneFeaturesForFoundAllele =
-                        gene.data.meta[metaKey.alleleMutationsReliableRegion]
-                            ?.map { GeneFeature.parse(it) }
-                            ?.sorted()
-                    when {
-                        geneFeaturesForFoundAllele != null -> {
-                            geneFeaturesForFoundAllele.forEach { geneFeature ->
-                                val range = gene.referencePoints.getRange(geneFeature)
-                                val sequence = gene.getFeature(geneFeature)
-                                writer.write(FastaRecord(id++, "${gene.name} $range $geneFeature", sequence))
-                            }
-                        }
-
-                        else -> {
-                            val range = Range(
-                                gene.referencePoints.firstAvailablePosition,
-                                gene.referencePoints.lastAvailablePosition
-                            )
-                            val sequence = gene.getSequence(range)
-                            writer.write(FastaRecord(id++, "${gene.name} $range", sequence))
-                        }
-                    }
+                    val range = Range(
+                        gene.referencePoints.firstAvailablePosition,
+                        gene.referencePoints.lastAvailablePosition
+                    )
+                    val sequence = gene.getSequence(range)
+                    writer.write(FastaRecord(id++, "${gene.name} $range", sequence))
                 }
         }
     }

From b409ce74d9a1be8ec38f94fcfeeda2585f74c4f5 Mon Sep 17 00:00:00 2001
From: gnefedev <georgynefedev@gmail.com>
Date: Wed, 5 Apr 2023 11:36:52 +0200
Subject: [PATCH 2/3] mandatory cup data for alleles search

---
 src/main/resources/parameters/find_alleles_parameters.json | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/main/resources/parameters/find_alleles_parameters.json b/src/main/resources/parameters/find_alleles_parameters.json
index 0c8509f97..c675d850c 100644
--- a/src/main/resources/parameters/find_alleles_parameters.json
+++ b/src/main/resources/parameters/find_alleles_parameters.json
@@ -8,6 +8,7 @@
       "useClonesWithCountGreaterThen": 1
     },
     "searchAlleleParameterForFirstRound": {
+      "clonesToSearchCap": 10000,
       "minClonesCountForAlleleSearch": 20,
       "topByScore": 0.3,
       "coefficientForNaiveClonesInScore": 2.0,
@@ -21,6 +22,7 @@
       "minCountOfNaiveClonesToAddAllele": 0
     },
     "searchAlleleParameterForSecondRound": {
+      "clonesToSearchCap": 10000,
       "minClonesCountForAlleleSearch": 10,
       "topByScore": 0.65,
       "coefficientForNaiveClonesInScore": 2.0,

From 0ffb6d6bc04aa593e73d5d81bcf3fde939c55682 Mon Sep 17 00:00:00 2001
From: gnefedev <georgynefedev@gmail.com>
Date: Wed, 5 Apr 2023 11:48:03 +0200
Subject: [PATCH 3/3] update versions

---
 build.gradle.kts | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/build.gradle.kts b/build.gradle.kts
index d6f16bed2..7386ff3c6 100644
--- a/build.gradle.kts
+++ b/build.gradle.kts
@@ -134,10 +134,10 @@ val toObfuscate: Configuration by configurations.creating {
 
 val obfuscationLibs: Configuration by configurations.creating
 
-val mixcrAlgoVersion = "4.3.0-41-develop"
-val milibVersion = "2.4.0-5-master"
+val mixcrAlgoVersion = "4.3.0-46-allele_fix"
+val milibVersion = "2.4.0-7-master"
 val mitoolVersion = "1.7.0-5-main"
-val repseqioVersion = "1.8.0-11-master"
+val repseqioVersion = "1.8.0-20-master"
 
 val picocliVersion = "4.6.3"
 val jacksonBomVersion = "2.14.2"